Biology subjects

Pecrix, Y.

Publications and source records attributed to Pecrix, Y..

3 recordsLinked to original sources

bioRxiv2025

Robust design and validation of LAMP assays for in-field detection of three major bacterial vascular diseases of banana

Bacterial diseases of banana are becoming increasingly significant worldwide, resulting in reduced yields and higher disease management costs. The most important bacterial diseases of banana include Moko and banana blood disease (BBD), caused by Ralstonia solanacearum and Ralstonia syzygii subsp. celebesensis, respectively, and banana Xanthomonas wilt (BXW) caused by Xanthomonas vasicola pv. musacearum. Effective surveillance and disease management require point-of-care diagnostics, such as loop-mediated isothermal amplification (LAMP), for on-site operation. In this study, three LAMP assays were developed to specifically detect the bacteria responsible for Moko, BBD and BXW, directly from banana tissues, using a simplified DNA extraction protocol. The BBD - and BXW-LAMP assays demonstrated 100% specificity, yielding negative results for a broad range of non-target bacteria, including closely related species as well as pathogenic and endophytic strains associated with banana, and positive results for all the tested target strains. For Moko disease, a duplex-LAMP assay was developed to detect all strains from the four globally most relevant sequevars: IIB-3, IIB-4, IIA-6, and IIA-24. The duplex-LAMP successfully detected all target strains, except one that was shown to be non-pathogenic to Cavendish bananas. All non-target strains tested negative, with the exception of a delayed signal for one strain belonging to Ralstonia thomasi, not associated with banana environment (hospital strain). These results were supported by an extensive in silico analysis conducted on 9,668 Burkholderiaceae and 7,483 Xanthomonadaceae genomes. Detection limits ranged from 0.1 pg/{micro}l to 1 pg/{micro}l DNA, and from 10 to 10 CFU/ml on banana tissues spiked with calibrated bacterial suspensions, depending on the assay. The LAMP assays prove highly effective for detecting target pathogens in both artificially inoculated banana plants and field samples, offering a promising tool for improving disease management strategies.

molecular biology↗

bioRxiv2024

Emergence and host range expansion of an epidemic lineage of Ralstonia solanacearum

The evolutionary processes underlying disease outbreaks remain unknown for most bacterial plant pathogens. We sequenced an outbreak of lethal wilt disease in Martinique caused by two distantly related lineages in the Ralstonia solanacearum species complex. One lineage (R. solanacearum IIB-4NPB) exhibited the broadest host range ever documented for a single lineage in the field, while the other (R. pseudosolanacearum I-18) expanded in parallel but retained specialisation on solanaceaous hosts. Phylogenomic analysis of 407 outbreak isolates shows both lineages independently disseminated from mainland populations into Martinique. We resolved fine-scale geographic patterns of genomic diversity and identified spatial hotspots of interspecies mobile element exchange, resulting in the identification of a new family of Ralstonia integrative conjugative elements (ICEs) associated with the outbreak. ICE accessory gene integration sites display striking functional specialization and differentiation despite variable gene content: each site acquires only metabolism-associated or defence-related genes, respectively. This work provides insight into the origin and genomic changes associated with an outbreak of plant disease, and highlights the role of mobile elements in driving pathogen emergence.

microbiology↗

bioRxiv2023

Evidence for increased fitness of a plant pathogen conferred by epigenetic variation

Adaptation is usually explained by adaptive genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, more and more studies show that genetic mutation analysis alone is not sufficient to fully explain the processes of adaptive evolution and report the existence of non-genetic (or epigenetic) inheritance and its significant role in the generation of adapted phenotypes. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia solanacearum to the host plant during an experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones that were obtained after serial passages on a given host plant during 300 generations, either on susceptible or tolerant hosts. Comparison with the methylome of the ancestral clone revealed between 12 and 21 differential methylated sites (DMSs) at the GTWWAC motif in the evolved clones. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential gene expression. Only one gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR (Methylation Sensitive Restriction Enzyme - qPCR) technology was used as an alternative approach to assess the methylation state of the DMSs found by SMRT-seq between the ancestral and evolved clones. This approach also found the two DMSs upstream of RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these two DMSs in host adaptation. As these DMSs appeared very quickly in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. To our knowledge, this is the first study showing a link between epigenetic variation and evolutionary adaptation to new environment.

evolutionary biology↗